CVS commit: pkgsrc/biology/biolibc

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Aug 12 14:49:18 UTC 2023

Modified Files:
        pkgsrc/biology/biolibc: Makefile PLIST buildlink3.mk distinfo

Log Message:
biology/biolibc: Update to 0.2.5

Make header files C++ compatible (extern C)
bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p
bl_gff_extract_attribute(): Improve performance
gff -> gff3 to distinguish from past and future GFF specs
Silence some compiler warnings

Changes: https://github.com/auerlab/biolibc/releases


To generate a diff of this commit:
cvs rdiff -u -r1.12 -r1.13 pkgsrc/biology/biolibc/Makefile
cvs rdiff -u -r1.11 -r1.12 pkgsrc/biology/biolibc/PLIST \
    pkgsrc/biology/biolibc/buildlink3.mk
cvs rdiff -u -r1.13 -r1.14 pkgsrc/biology/biolibc/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/biology/biolibc/Makefile
diff -u pkgsrc/biology/biolibc/Makefile:1.12 pkgsrc/biology/biolibc/Makefile:1.13
--- pkgsrc/biology/biolibc/Makefile:1.12        Wed Jun 14 18:41:24 2023
+++ pkgsrc/biology/biolibc/Makefile     Sat Aug 12 14:49:18 2023
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.12 2023/06/14 18:41:24 bacon Exp $
+# $NetBSD: Makefile,v 1.13 2023/08/12 14:49:18 bacon Exp $
 
-DISTNAME=      biolibc-0.2.4.3
+DISTNAME=      biolibc-0.2.5
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG=    3dc616d0903a024cb48f5f646680edf62c9eeeb1
 
 OWNER=         bacon%NetBSD.org@localhost
 HOMEPAGE=      https://github.com/auerlab/biolibc

Index: pkgsrc/biology/biolibc/PLIST
diff -u pkgsrc/biology/biolibc/PLIST:1.11 pkgsrc/biology/biolibc/PLIST:1.12
--- pkgsrc/biology/biolibc/PLIST:1.11   Wed Jun 14 18:41:24 2023
+++ pkgsrc/biology/biolibc/PLIST        Sat Aug 12 14:49:18 2023
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.11 2023/06/14 18:41:24 bacon Exp $
+@comment $NetBSD: PLIST,v 1.12 2023/08/12 14:49:18 bacon Exp $
 include/biolibc/align-accessors.h
 include/biolibc/align-mutators.h
 include/biolibc/align-rvs.h
@@ -21,14 +21,14 @@ include/biolibc/fastx-accessors.h
 include/biolibc/fastx-mutators.h
 include/biolibc/fastx-rvs.h
 include/biolibc/fastx.h
-include/biolibc/gff-accessors.h
-include/biolibc/gff-index-accessors.h
-include/biolibc/gff-index-mutators.h
-include/biolibc/gff-index-rvs.h
-include/biolibc/gff-index.h
-include/biolibc/gff-mutators.h
-include/biolibc/gff-rvs.h
-include/biolibc/gff.h
+include/biolibc/gff3-accessors.h
+include/biolibc/gff3-index-accessors.h
+include/biolibc/gff3-index-mutators.h
+include/biolibc/gff3-index-rvs.h
+include/biolibc/gff3-index.h
+include/biolibc/gff3-mutators.h
+include/biolibc/gff3-rvs.h
+include/biolibc/gff3.h
 include/biolibc/overlap-accessors.h
 include/biolibc/overlap-mutators.h
 include/biolibc/overlap-rvs.h
@@ -322,61 +322,61 @@ man/man3/bl_fastx_set_fasta.3
 man/man3/bl_fastx_set_fastq.3
 man/man3/bl_fastx_set_format.3
 man/man3/bl_fastx_write.3
-man/man3/bl_gff_copy.3
-man/man3/bl_gff_copy_header.3
-man/man3/bl_gff_dup.3
-man/man3/bl_gff_extract_attribute.3
-man/man3/bl_gff_free.3
-man/man3/bl_gff_index_add.3
-man/man3/bl_gff_index_seek_reverse.3
-man/man3/bl_gff_index_set_array_size.3
-man/man3/bl_gff_index_set_count.3
-man/man3/bl_gff_index_set_end.3
-man/man3/bl_gff_index_set_end_ae.3
-man/man3/bl_gff_index_set_end_cpy.3
-man/man3/bl_gff_index_set_file_pos.3
-man/man3/bl_gff_index_set_file_pos_ae.3
-man/man3/bl_gff_index_set_file_pos_cpy.3
-man/man3/bl_gff_index_set_seqid.3
-man/man3/bl_gff_index_set_seqid_ae.3
-man/man3/bl_gff_index_set_seqid_cpy.3
-man/man3/bl_gff_index_set_start.3
-man/man3/bl_gff_index_set_start_ae.3
-man/man3/bl_gff_index_set_start_cpy.3
-man/man3/bl_gff_init.3
-man/man3/bl_gff_read.3
-man/man3/bl_gff_sam_cmp.3
-man/man3/bl_gff_sam_overlap.3
-man/man3/bl_gff_set_attributes.3
-man/man3/bl_gff_set_attributes_ae.3
-man/man3/bl_gff_set_attributes_array_size.3
-man/man3/bl_gff_set_attributes_cpy.3
-man/man3/bl_gff_set_attributes_len.3
-man/man3/bl_gff_set_end.3
-man/man3/bl_gff_set_feature_id.3
-man/man3/bl_gff_set_feature_id_ae.3
-man/man3/bl_gff_set_feature_id_cpy.3
-man/man3/bl_gff_set_feature_name.3
-man/man3/bl_gff_set_feature_name_ae.3
-man/man3/bl_gff_set_feature_name_cpy.3
-man/man3/bl_gff_set_feature_parent.3
-man/man3/bl_gff_set_feature_parent_ae.3
-man/man3/bl_gff_set_feature_parent_cpy.3
-man/man3/bl_gff_set_file_pos.3
-man/man3/bl_gff_set_gene_name_cpy.3
-man/man3/bl_gff_set_phase.3
-man/man3/bl_gff_set_score.3
-man/man3/bl_gff_set_seqid_ae.3
-man/man3/bl_gff_set_seqid_cpy.3
-man/man3/bl_gff_set_source_ae.3
-man/man3/bl_gff_set_source_cpy.3
-man/man3/bl_gff_set_start.3
-man/man3/bl_gff_set_strand.3
-man/man3/bl_gff_set_type_ae.3
-man/man3/bl_gff_set_type_cpy.3
-man/man3/bl_gff_skip_header.3
-man/man3/bl_gff_to_bed.3
-man/man3/bl_gff_write.3
+man/man3/bl_gff3_copy.3
+man/man3/bl_gff3_copy_header.3
+man/man3/bl_gff3_dup.3
+man/man3/bl_gff3_extract_attribute.3
+man/man3/bl_gff3_free.3
+man/man3/bl_gff3_index_add.3
+man/man3/bl_gff3_index_seek_reverse.3
+man/man3/bl_gff3_index_set_array_size.3
+man/man3/bl_gff3_index_set_count.3
+man/man3/bl_gff3_index_set_end.3
+man/man3/bl_gff3_index_set_end_ae.3
+man/man3/bl_gff3_index_set_end_cpy.3
+man/man3/bl_gff3_index_set_file_pos.3
+man/man3/bl_gff3_index_set_file_pos_ae.3
+man/man3/bl_gff3_index_set_file_pos_cpy.3
+man/man3/bl_gff3_index_set_seqid.3
+man/man3/bl_gff3_index_set_seqid_ae.3
+man/man3/bl_gff3_index_set_seqid_cpy.3
+man/man3/bl_gff3_index_set_start.3
+man/man3/bl_gff3_index_set_start_ae.3
+man/man3/bl_gff3_index_set_start_cpy.3
+man/man3/bl_gff3_init.3
+man/man3/bl_gff3_read.3
+man/man3/bl_gff3_sam_cmp.3
+man/man3/bl_gff3_sam_overlap.3
+man/man3/bl_gff3_set_attributes.3
+man/man3/bl_gff3_set_attributes_ae.3
+man/man3/bl_gff3_set_attributes_array_size.3
+man/man3/bl_gff3_set_attributes_cpy.3
+man/man3/bl_gff3_set_attributes_len.3
+man/man3/bl_gff3_set_end.3
+man/man3/bl_gff3_set_feature_id.3
+man/man3/bl_gff3_set_feature_id_ae.3
+man/man3/bl_gff3_set_feature_id_cpy.3
+man/man3/bl_gff3_set_feature_name.3
+man/man3/bl_gff3_set_feature_name_ae.3
+man/man3/bl_gff3_set_feature_name_cpy.3
+man/man3/bl_gff3_set_feature_parent.3
+man/man3/bl_gff3_set_feature_parent_ae.3
+man/man3/bl_gff3_set_feature_parent_cpy.3
+man/man3/bl_gff3_set_file_pos.3
+man/man3/bl_gff3_set_gene_name_cpy.3
+man/man3/bl_gff3_set_phase.3
+man/man3/bl_gff3_set_score.3
+man/man3/bl_gff3_set_seqid_ae.3
+man/man3/bl_gff3_set_seqid_cpy.3
+man/man3/bl_gff3_set_source_ae.3
+man/man3/bl_gff3_set_source_cpy.3
+man/man3/bl_gff3_set_start.3
+man/man3/bl_gff3_set_strand.3
+man/man3/bl_gff3_set_type_ae.3
+man/man3/bl_gff3_set_type_cpy.3
+man/man3/bl_gff3_skip_header.3
+man/man3/bl_gff3_to_bed.3
+man/man3/bl_gff3_write.3
 man/man3/bl_next_start_codon.3
 man/man3/bl_next_stop_codon.3
 man/man3/bl_overlap_print.3
Index: pkgsrc/biology/biolibc/buildlink3.mk
diff -u pkgsrc/biology/biolibc/buildlink3.mk:1.11 pkgsrc/biology/biolibc/buildlink3.mk:1.12
--- pkgsrc/biology/biolibc/buildlink3.mk:1.11   Wed Jun 14 18:41:24 2023
+++ pkgsrc/biology/biolibc/buildlink3.mk        Sat Aug 12 14:49:18 2023
@@ -1,11 +1,11 @@
-# $NetBSD: buildlink3.mk,v 1.11 2023/06/14 18:41:24 bacon Exp $
+# $NetBSD: buildlink3.mk,v 1.12 2023/08/12 14:49:18 bacon Exp $
 
 BUILDLINK_TREE+=       biolibc
 
 .if !defined(BIOLIBC_BUILDLINK3_MK)
 BIOLIBC_BUILDLINK3_MK:=
 
-BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.4.3
+BUILDLINK_API_DEPENDS.biolibc+=        biolibc>=0.2.5
 BUILDLINK_PKGSRCDIR.biolibc?=  ../../biology/biolibc
 
 .include "../../devel/libxtend/buildlink3.mk"

Index: pkgsrc/biology/biolibc/distinfo
diff -u pkgsrc/biology/biolibc/distinfo:1.13 pkgsrc/biology/biolibc/distinfo:1.14
--- pkgsrc/biology/biolibc/distinfo:1.13        Wed Jun 14 18:41:24 2023
+++ pkgsrc/biology/biolibc/distinfo     Sat Aug 12 14:49:18 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.13 2023/06/14 18:41:24 bacon Exp $
+$NetBSD: distinfo,v 1.14 2023/08/12 14:49:18 bacon Exp $
 
-BLAKE2s (biolibc-0.2.4.3-3dc616d0903a024cb48f5f646680edf62c9eeeb1.tar.gz) = 61670347aa31e917a033129b1b227b6dd60c7e50d5f9e1979e4aee9c23cb3af3
-SHA512 (biolibc-0.2.4.3-3dc616d0903a024cb48f5f646680edf62c9eeeb1.tar.gz) = 
af53733a126b224e3b195a20dc8bfcbb250d5bd2e2526db10e941cbda3ec730f9f431522bb4b5d1564481d11dcdf16848e46ad544f151e2a78d89a4dc76ab6a8
-Size (biolibc-0.2.4.3-3dc616d0903a024cb48f5f646680edf62c9eeeb1.tar.gz) = 141047 bytes
+BLAKE2s (biolibc-0.2.5.tar.gz) = ea2f46e8c6b26da34c2d10603ae1974e680e5df3a1ce8110235dc1afe1d24ec5
+SHA512 (biolibc-0.2.5.tar.gz) = 647d8b19d007775f140b4b2d23bc8048ee6896e34b2d046109c71b1be13955a79991bb7dfbda8887db852265825d18b58e16195173624efb9bd19e6d1f5d13ba
+Size (biolibc-0.2.5.tar.gz) = 141426 bytes